Fig. 5: LOH of HLA-I and neoepitope load.
From: Genetic immune escape landscape in primary and metastatic cancer
a, Visual depiction of the neoepitope (neo.) allele ratio and its significance (partially created with BioRender.com). b, Top, number of allele pairs in each neoepitope allele ratio bucket in metastatic samples harboring LOH of HLA-I. Bottom, representation of the mean observed (black) and randomized (blue) neoepitope allele ratio across 100 bootstraps (thicker lines). The vertical error bars represent the s.d. of the neoepitope allele ratio. The narrow black lines represent the observed neoepitope allele ratio values across the 100 bootstraps. P values were calculated using the two-sample Kolmogorov–Smirnov test for goodness of fit. c, Analogous to b for the primary PCAWG dataset. d,e, Similar representation but subsampling for focal LOH of HLA-I in metastatic (Hartwig) (d) and primary (PCAWG) (e) datasets, respectively. f,g, Similar representation but subsampling for nonfocal LOH of HLA-I: metastatic (Hartwig) (f) and primary (PCAWG) (g) tumor datasets.
